lean codes, traction control light, hard shifts???

I have an '06 gtp sedan, with the 3.9 automatic. I've taken the car to the dealer because driving down the road one day the traction control light came on in the dash. I noticed that while the light was on the transmission shifts hard. It did it one time at a stop light, and when i took off it was like you neutral dropped it, with a nice clunk when it went into gear. After this happens the cel comes on. The dealer told me that the k&n air filter was the problem and I had to clean my MAF sensor. I replaced the k&n with a conventional filter, and cleaned the MAF sensor. The car is worse than ever, of course this all occurred right at the 100000 mile mark, and now the car is over and there is no sense in taking the car back to HALEY they suck as far as service. Any help at all would be appreciated